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| Number | Name | Type | Year | Researchgate | Endnote | |
|---|---|---|---|---|---|---|
| 1 | Zongliang Yue, Christopher D Willey, Anita B Hjelmeland, and Jake Y. Chen* (2019) BEERE: a web server for biomedical entity expansion, ranking and explorations. Nucleic Acids Research, gkz428 | Refereed –Journal Articles | 2019 | |||
| 2 | Xiaowen Liu, Zongliang Yue, Yimou Cao, Lauren Taylor, Qing Zhang, Sung Wong Choi, Samir Hanash, Sawa Ito, Jake Y Chen, Huanmei Wu, and Sophie Paczesny (2019) A GVHD-free Antitumoral Signature Following Allogeneic Donor Lymphocyte Injection Identified by Proteomics and Systems Biology. JCO Precision Oncology, Vol. 3, pp 1-11. | Refereed –Journal Articles | 2019 | |||
| 3 | Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y Chen, Yueping Shen, Nengjun Yi (2019) Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. BMC Bioinformatics, Vol. 20, p. 94. doi.org/10.1186/s12859-019-2656-1 | Refereed –Journal Articles | 2019 | |||
| 4 | Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, and Jake Y. Chen (2019) Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. ACM/IEEE Transactions on Computational Biology and Bioinformatics, (in press) | Refereed –Journal Articles | 2019 | |||
| 5 | Syed Aun Muhammad*, Nighat Fatima, Rehan Zafar Paracha, Amjad Ali, and Jake Y. Chen* (2019) A Systematic Simulation-based Meta-analytical Framework for Prediction of Physiological Biomarkers in Alopecia. Journal of Biological Research-Thessaloniki, Vol. 26, No. 2, doi.org/10.1186/s40709-019-0094-x. | Refereed –Journal Articles | 2019 | |||
| 6 | Xin Gao, Jake Y. Chen, and Mohammed J. Zaki (2018) Multiscale and Multimodal Analysis for Computational Biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 15, No. 6, pp. 1951-1952 | Refereed –Journal Articles | 2018 | |||
| 7 | Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen* (2018) “Super Gene Set” Causal Relationship Discovery from Functional Genomics Data. ACM/IEEE Transactions on Computational Biology and Bioinformatics, Vol. 15, No. 6, pp. 1991-1998. | Refereed –Journal Articles | 2018 | |||
| 8 | Wuqiang Zhu, Eric Zhang, Meng Zhao, Zechen Chong, Chengming Fan, Yawen Tang, Jervaughn D. Hunter, Anton V. Borovjagin, Greggory P. Walcott, Jake Y. Chen, Gangjian Qin, Jianyi Zhang (2018) Regenerative Potential of Neonatal Porcine Hearts. Circulation, Vol. 138, No. 24, pp. 2809-2816. | Refereed –Journal Articles | 2018 | |||
| 9 | Syed Aun Muhammad*, Jinlei Guo, Thanh Minh Nguyen, Xiaogang Wu, Baogang Bai, X Frank Yang, Jake Y. Chen* (2018) Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins. Frontiers in Microbiology, Vol. 9, No. 380, doi:10.3389/fmicb.2018.00380. | Refereed –Journal Articles | 2018 | |||
| 10 | Zongliang Yue, Qi Zheng, Micheal T Neylong, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, and Jake Y. Chen* (2018) PAGER 2.0: An Update to the Pathway, Annotated-list, and Gene-signature Electronic Repository for Network Biology. Nucleic Acids Research, Vol. 46, No. D1, pp. D668-D676. | Refereed –Journal Articles | 2018 | |||
| 11 | Zongliang Yue, Itika Arora, Eric Zhang, Vincent Laufer, S. Louis Bridges, and Jake Y. Chen* (2017) Repositioning Drugs by Targeting Network Modules: A Parkinson’s Disease Case Study. BMC Bioinformatics, Vol. 18, Suppl 14, 532. | Refereed –Journal Articles | 2017 | |||
| 12 | Baron Arnone, Jake Y. Chen, and Gangjian Qin (2017) Characterization and Analysis of Long Non-Coding RNA (lncRNA) in in vitro- and ex vivo-derived Cardiac Progenitor Cells. PLOS ONE, Vol. 12, No. 6, e0180096. | Refereed –Journal Articles | 2017 | |||
| 13 | Vincent A. Laufer, Jake Y. Chen, S Louis Bridges Jr (2017) Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases. Rheumatic Disease Clinics, Vol. 43, No. 3, pp. 449-466. | Refereed –Journal Articles | 2017 | |||
| 14 | Jake Y. Chen*, Ragini Pandey, and Thanh Nguyen (2017) HAPPI-2: Constructing a Comprehensive Map of Human Annotated and Predicted Protein Interactions. BMC Genomics, Vol. 18, 182. | Refereed –Journal Articles | 2017 | |||
| 15 | Syed Aun Muhammad*, Waseem Raza, Thanh Nguyen, Baogang Bai, Xiaogang Wu, and Jake Chen* (2017) Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus. Frontiers in Physiology, Vol. 8, No. 13, doi:10.3389/fphys.2017.00013. | Refereed –Journal Articles | 2017 | |||
| 16 | Fan Zhang and Jake Y. Chen* (2016) A Method for Identifying Discriminative Isoform-Specific Peptides for Clinical Proteomics Application. BMC Genomics, Vol. 17, Suppl. 7, 522. | Refereed –Journal Articles | 2016 | |||
| 17 | Xiaowen Liu, Zongliang Yue, Jeffrey Yu, Etienne Daguindau, KushiKushekhar, Qing Zhang, Yuko Ogata, Philip Gafken, Yoshihiro Inamota, Adam Gracon, David Wikes, John Hansen, Stephanie Lee, Jake Y. Chen, and Sophie Paczesny* (2016) Proteomic characterization reveals that MMP-3 correlates with bronchiolitis obliterans syndrome following allogeneic hematopoietic cell and lung transplantation, American Journal of Transplantation, Vol. 16, No. 8, pp. 2342-2351. | Refereed –Journal Articles | 2016 | |||
| 18 | Syed Aun Muhammad, Nighat Fatima, Nawazish-i-Husain Syed, XiaogangWu, X. Frank Yang, and Jake Y. Chen* (2015) MicroRNA Expression Profiling of Human Respiratory Epithelium Affected by Invasive Candida infection. PLOS ONE, Vol. 10, No. 8, e0136454. | Refereed –Journal Articles | 2015 | |||
| 19 | Zongliang Yue, Madhura Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael Neylon, Liugen Zhu, Timothy Ratliff, and Jake Y. Chen* (2015) PAGER: Constructing PAGs and new PAG-PAG Relationships for Network Biology. ISMB/ECCB Special Issue, Bioinformatics, Vol. 31, No. 12, pp. i250-i257. | Refereed –Journal Articles | 2015 | |||
| 20 | Hui Huang, Thanh Nguyen, Sara Ibrahim, and Jake Y. Chen* (2015) DMAP: A next-generation connectivity map database towards drug repositioning applications. MCBIOS ’15 Special Issue, BMC Bioinformatics, Vol. 16, Suppl. 13, S4 | Refereed –Journal Articles | 2015 | |||
| 21 | Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen* (2015) A Method for Developing Regulatory Gene Set Networks to Characterize Complex Biological Systems. BMC Genomics, Vol. 16, Suppl. 11, S4 (IF = 4.07) | Refereed –Journal Articles | 2015 | |||
| 22 | Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki (2015) Knowledge Discovery Using Big Data in Biomedical Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 12, No. 4, pp. 726-729. | Refereed –Journal Articles | 2015 | |||
| 23 | Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie, and Jake Y. Chen* (2014) SLDR: A Computational Technique to Identify Novel Genetic Regulatory Relationship. BMC Bioinformatics, Vol. 15, Suppl. 11, S1 (received the best paper award out of >60 submissions) | Refereed –Journal Articles | 2014 | |||
| 24 | Syed Aun Muhammad, Safia Ahmed, Amjad Ali, Hui Huang, Xiaogang Wu, X. Frank Yang, Anam Naz, Jake Y. Chen* (2014) Prioritizing Drug Targets in Clostridium botulinum with a Computational Systems Biology Approach. Genomics, Vol. 104, No. 1, pp. 24-35. | Refereed –Journal Articles | 2014 | |||
| 25 | Xiaogang Wu, Mohammad Al Hasan, and Jake Y. Chen* (2014) Pathway and Network Analysis in Proteomics. Journal of Theoretical Biology, Vol. 362, pp. 44-52. | Refereed –Journal Articles | 2014 | |||
| 26 | Zongliang Yue, Zhan Xie, Ping Wan and Jake Y. Chen (2014) Computational Identification of De-centric Genetic Regulatory Relationships from Functional Genomic Data, Lecture Notes in Bioinformatics, Vol. 8492, pp. 224-235. | Refereed –Journal Articles | 2014 | |||
| 27 | Tianxiao Huan, Xiaogang Wu, Zengliang Bai*, and Jake Y. Chen* (2014) Seed-weighted Random Walk Ranking for Cancer Biomarker Prioritization: a Case Study in Leukemia. International Journal of Data Mining and Bioinformatics, Vol. 9, No. 2, pp.135-148. | Refereed –Journal Articles | 2014 | |||
| 28 | Shubo Zhang, Jake Y. Chen, Jianan Rao, Shanghong Zhang, Daniel Wai Tin Chan, Guanghua Liu, Yang Xu, and Miao He (2014) Genetic Variation Analysis of Hemagglutinin and Neuraminidase of Human Influenza A (H3N2) Virus in Hong Kong (1997-2006). African Journal of Microbiology Research, Vol. 8, No. 18, pp. 1863-1898. | Refereed –Journal Articles | 2014 | |||
| 29 | Jake Y. Chen, Micheline Piquette-Miller, and BP Smith (2013) Network Medicine: Finding the Links to Personalized Therapy. Clinical Pharmacology & Therapeutics, Vol. 94, No. 6, pp. 613-615. | Refereed –Journal Articles | 2013 | |||
| 30 | Fan Zhang, Jake Chen, Mu Wang, and Renee Drabier (2013) A Neural Network Approach to Multi-biomarker Panel Discovery by High-throughput Plasma Proteomics Profiling of Breast Cancer. BMC Proceedings, Vol. 7, Suppl. 7, S10. | Refereed –Journal Articles | 2013 | |||
| 31 | Huajun Chen*, Tong Yu*, and Jake Y. Chen* (2013) Semantic Web Meets Integrative Biology: A Survey. Briefings in Bioinformatics, Vol. 14, No. 1, pp. 109-125. | Refereed –Journal Articles | 2013 | |||
| 32 | Liang-Chin Huang, Xiaogang Wu, and Jake Y. Chen* (2013) Predicting Adverse Drug Reaction Profiles by Integrating Protein Interaction Networks with Drug Structures. Proteomics, Vol. 13, No. 2, pp. 313-324. (IF = 4.51) | Refereed –Journal Articles | 2013 | |||
| 33 | Fan Zhang and Jake Y. Chen* (2013) Breast Cancer Subtyping from Plasma Proteins. BMC Medical Genomics, Vol 6, Suppl. 1, S6. | Refereed –Journal Articles | 2013 | |||
| 34 | Hui Huang, Xiaogang Wu, Ragini Pandey, Jiao Li, Guoling Zhao, Sara Ibrahim, Jake Y. Chen* (2012) C2Maps: A Network Pharmacology Database with Comprehensive Disease-Gene-Drug Connectivity Relationships. BMC Genomics, Vol. 13, Suppl. 6, S17. | Refereed –Journal Articles | 2012 | |||
| 35 | Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan*, Jake Y. Chen* (2012) PAGED: A Pathway and Gene-set Enrichment Database to Enable Molecular Phenotype Discoveries. BMC Bioinformatics, Vol. 13, Suppl. 15, S2. (IF = 2.75) | Refereed –Journal Articles | 2012 | |||
| 36 | Paul Hale, Alfredo M. López-Yunez, Jake Y. Chen* (2012) Genome-wide Meta-analysis of Genetic Susceptible Genes for Type-2 Diabetes, BMC Systems Biology, Vol. 6, Suppl. 3, S16. | Refereed –Journal Articles | 2012 | |||
| 37 | Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li*, and Jake Y. Chen* (2012) Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays. Journal of Integrative Bioinformatics, Vol. 9, No. 2, 213. | Refereed –Journal Articles | 2012 | |||
| 38 | John Springer, Fan Zhang, Peter Hussey, Charles Buck, Fred Regnier, and Jake Y. Chen* (2012) Towards a Metadata Model for Mass-Spectrometry Based Clinical Proteomics. Current Bioinformatics, Vol. 7, No. 3, pp. 246-254. | Refereed –Journal Articles | 2012 | |||
| 39 | Mohammad Al Hasan, Jun Huan, Jake Chen, and Mohammed J. Zaki (2012) Biological Knowledge and Data Mining: An Editorial. Scientific Programming, Vol. 20, No. 1, pp. 1-2. | Refereed –Journal Articles | 2012 | |||
| 40 | Liang-Chin Huang, Xiaogang Wu, and Jake Y. Chen* (2011) Predicting Adverse Side Effects of Drugs. BMC Genomics, Vol. 12, Suppl. 5, S11. | Refereed –Journal Articles | 2011 | |||
| 41 | Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, and Jake Y. Chen* (2011) Reordering Based Integrative Expression Profiling for Microarray Classification. BMC Bioinformatics, Vol. 13, Suppl. 2, S1. (IF = 3.03) | Refereed –Journal Articles | 2011 | |||
| 42 | Jiliang Li, Fan Zhang, and Jake Y. Chen* (2011) An Integrated Proteomics Analysis of Bone Tissues in Response to Mechanical Stimulation. BMC Systems Biology, Vol. 5, Suppl. 3, S7. | Refereed –Journal Articles | 2011 | |||
| 43 | Fan Zhang and Jake Y. Chen* (2011) HOMER: A Human Organ-specific Molecular Electronic Repository. BMC Bioinformatics, Vol. 12, Suppl. 10, S4. | Refereed –Journal Articles | 2011 | |||
| 44 | Fengjun Li, Xukai Zou, Peng Liu, and Jake Y. Chen* (2011) New Threats to Health Data Privacy. BMC Bioinformatics, Vol. 12, Suppl. 12, S7. (IF = 3.03) | Refereed –Journal Articles | 2011 | |||
| 45 | Lijie Sun, Hong-Mei Li, Manfredo J. Seufferheld, Kent Walters, Venu Margam, Amber Jannasch, Naomi Diaz, Catherine P. Riley, Weilin Sun, Yueh-Feng Li, William M. Muir, Jun Xie, Jing Wu, Fan Zhang, Jake Y. Chen, Eric L. Barker, Jiri Adamec, & Barry R. Pittendrigh (2011) Systems-scale analysis reveals pathways involved in cellular response to methamphetamine. PLOS ONE, 6(4): e18215. | Refereed –Journal Articles | 2011 | |||
| 46 | Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, and Jake Y. Chen* (2011) Computational analysis of drought-stress associated miRNAs and miRNA co-regulation network in Physcomitrella patens. Bioinformatics, Genomics, and Proteomics, Vol. 9, No. 1-2, pp. 37-44. | Refereed –Journal Articles | 2011 | |||
| 47 | Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S. Wilbanks, Barbara Lynn Escalon, Sharon A. Meyer, Edward J. Perkins, and Jake Y. Chen* (2010) A new Approach to Construct Pathway Connected Networks and Its Application in Dose Responsive Gene Expression Profiles of Rat Liver Regulated by 2,4DNT. BMC Genomics, Vol. 11, Suppl. 3, S4. | Refereed –Journal Articles | 2010 | |||
| 48 | Fan Zhang and Jake Y. Chen* (2010) Discovery of Pathway Biomarkers from Coupled Proteomics and Systems Biology Methods. BMC Genomics, Vol. 11, Suppl. 2, S12 | Refereed –Journal Articles | 2010 | |||
| 49 | Ao Zhou, Fan Zhang, and Jake Y. Chen* (2010) PEPPI: A Peptidomic Database of Human Protein Isoforms for Proteomics Experiments. BMC Bioinformatics, Vol. 11, Suppl. 6, S7 | Refereed –Journal Articles | 2010 | |||
| 50 | Steve Naylor and Jake Y. Chen* (2010) Unraveling Human Complexity and Disease with Systems Biology and Personalized Medicine. Personalized Medicine, Vol. 7, No. 3, pp. 275-289 | Refereed –Journal Articles | 2010 | |||
| 51 | Tianxiao Huan, Xiaogang Wu, and Jake Y. Chen* (2010) Systems Biology Visualization Tools for Drug Target Discovery. Expert Opinion on Drug Discovery, Vol. 5, No. 5, pp. 425-439. | Refereed –Journal Articles | 2010 | |||
| 52 | Hong-Mei Li, Lijie Sun, Omprakash Mittapalli, William M. Muir, Jun Xie, Jing Wu, Brandon J. Schemerhorn, Amber Jannasch, Jake Y. Chen, Fan Zhang, Jiri Adamec, Larry L. Murdock, and Barry R. Pittendrigh (2010) Bowman-Birk Inhibitor Affects Pathways Associated with Energy Metabolism in Drosophila melanogaster. Insect Molecular Biology, Vol. 19, No. 3, pp. 303-313 | Refereed –Journal Articles | 2010 | |||
| 53 | Stefano Lonardi and Jake Y. Chen* (2010) Data Mining in Bioinformatics: Selected Papers from BIOKDD 2008. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 2, pp. 1-2. | Refereed –Journal Articles | 2010 | |||
| 54 | Mingyi Wang and Jake Y. Chen* (2010) A GMM-IG Framework for Selecting Genes as Expression Panel Biomarkers. Artificial Intelligence in Medicine, Vol. 48, No. 2-3, pp.75-82. | Refereed –Journal Articles | 2010 | |||
| 55 | Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* (2010) Discovering Novel Breast Cancer Drug Candidates from Biomedical Literature. International Journal of Data Mining and Bioinformatics. Vol. 4, No. 3, pp.241-255. | Refereed –Journal Articles | 2010 | |||
| 56 | Qian You, Shiaofen Fang, and Jake Y. Chen* (2010) GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks. Information Visualization, Vol. 9, No. 1, pp.1-12. | Refereed –Journal Articles | 2010 | |||
| 57 | Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* (2009) Building Disease-specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts. PLoS Computational Biology, Vol. 5, No. 7: e1000450. | Refereed –Journal Articles | 2009 | |||
| 58 | Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, and Jake Y. Chen* (2009) HPD: An Online Integrated Human Pathway Database Enabling Systems Biology Studies. BMC Bioinformatics, Vol. 10, Suppl. 11, S5 | Refereed –Journal Articles | 2009 | |||
| 59 | Jake Y. Chen*, SudhaRani Mamidipalli, and Tianxiao Huan (2009) HAPPI: an Online Database of Comprehensive Human Annotated and Predicted Protein Interactions. BMC Genomics, Vol. 10, Suppl. 1, S16. | Refereed –Journal Articles | 2009 | |||
| 60 | Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshu Zhou, and Jake Y. Chen* (2009) Finding Fractal Patterns in Molecular Interaction Networks: a Case Study in Alzheimer’s Disease. International Journal of Computational Biology and Drug Design, Vol. 2, No. 4, pp. 340-352. | Refereed –Journal Articles | 2009 | |||
| 61 | Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, and Jake Y. Chen* (2009) Semantic Graph Mining for Biomedical Network Analysis: an Overview. Briefings in Bioinformatics, Vol. 10, No. 2, pp. 177-192. | Refereed –Journal Articles | 2009 | |||
| 62 | Huian Li and Jake Y. Chen* (2009) Improved Biomedical Document Retrieval System with PubMed Term Statistics and Expansions. International Journal of Computational Intelligence in Bioinformatics and Systems Biology, Vol. 1, No. 1, pp. 74-85. | Refereed –Journal Articles | 2009 | |||
| 63 | Sudipto Saha, Scott H. Harrison, and Jake Y. Chen* (2009) Dissecting the Human Plasma Proteome and Inflammatory Response Biomarkers. Proteomics, Vol. 9, No. 2, pp. 470-484. | Refereed –Journal Articles | 2009 | |||
| 64 | Jake Y. Chen, Mohammed Zaki, and Stefano Lonardi (2008) BIOKDD 2008: A Workshop Report on Data Mining in Bioinformatics. SIGKDD Explorations, Vol. 10, No. 2, pp. 51-53. | Refereed –Journal Articles | 2008 | |||
| 65 | Tianxiao Huan, Andrey Sivachenko, Scott H. Harrison, and Jake Y. Chen* (2008) ProteoLens: a Visual Analytic Tool for Multi-scale Database-driven Biological Network Data Mining. BMC Bioinformatics, Vol. 9, S5, pp. 1-13. | Refereed –Journal Articles | 2008 | |||
| 66 | Sudipto Saha, Scott H. Harrison, Changyu Shen, Haixu Tang, Predrag Radivojac, Randy J. Arnold, Xiang Zhang, and Jake Y. Chen* (2008) HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals. BMC Medical Genomics, 2008, Vol. 1, 12. | Refereed –Journal Articles | 2008 | |||
| 67 | Stefano Lonardi and Jake Y. Chen* (2008) International Workshop on Data Mining in Bioinformatics (BIOKDD) 2007: Introduction. Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6, pp. v-vi. | Refereed –Journal Articles | 2008 | |||
| 68 | Lee W. Ott, Katheryn A. Resing, Alecia W. Sizemore, Joshua W. Heyen, Ross R. Cocklin, Nathan M. Pedrick, H. Cary Woods, Jake Y. Chen, Mark G. Goebl, Frank A. Witzmann, and Maureen A. Harrington (2007) Tumor Necrosis Factor-alpha and Interleukin-1 Induced Cellular Responses: Coupling Proteomic and Genomic Information. Journal of Proteome Research, Vol. 6, Issue 6, pp. 2176-2185. | Refereed –Journal Articles | 2007 | |||
| 69 | Lavanya Dhanapalan and Jake Y. Chen* (2007) A Case Study of Integrating Protein Interaction Data using Semantic Web Technology. International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 286-302. | Refereed –Journal Articles | 2007 | |||
| 70 | Jake Y. Chen*, Zhong Yan, Changyu Shen, Dawn P. G. Brown, and Mu Wang (2007) A Systems Biology Approach to The Study of Cisplatin Drug Resistance In Ovarian Cancers. Journal of Bioinformatics and Computational Biology, Vol. 5, Issue 02A, pp. 383-405. | Refereed –Journal Articles | 2007 | |||
| 71 | Megan Sickmeier, Justin Hamilton, Tanguy LeGall, Vladimir Vacic, Marc Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir Uversky, Zoran Obradovic, A Keith Dunker (2007) DisProt: The Database of Disordered Proteins. Nucleic Acids Research, Vol. 35 (Database issue): pp. 786-93. | Refereed –Journal Articles | 2007 | |||
| 72 | Tharam S. Dillon, Elizabeth Chang, Amandeep S. Sidhu, and Jake Y. Chen* (2007) Ontologies for Bioinformatics I. International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 261-267. | Refereed –Journal Articles | 2007 | |||
| 73 | Zsuzsanna Dosztányi, Jake Y. Chen, A. Keith Dunker, István Simon, and Peter Tompa (2006) Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution, Journal of Proteome Research, Vol. 5, Issue 11, pp. 2985-2995. | Refereed –Journal Articles | 2006 | |||
| 74 | Changyu Shen, Lang Li, Jake Y. Chen* (2006) A Statistical Framework to Discover True Associations from Multi-protein Complex Pull-down Proteomics Data Sets. Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 2, pp. 436-43. | Refereed –Journal Articles | 2006 | |||
| 75 | Jake Y. Chen* and Andrey Y. Sivachenko (2005) Data Mining in Protein Interactomics. IEEE Magazine in Biology and Medicine, Vol. 24, No. 3, pp. 95-102. | Refereed –Journal Articles | 2005 | |||
| 76 | Susie Stephens, Jake Y. Chen, Marcel Davidson, Shiby Thomas, and Barry M. Trute (2005) Oracle Database 10g: A Platform for BLAST Search and Regular Expression Pattern Matching in Life Sciences, Nucleic Acids Research, Vol. 33, Database Issue, pp. 675-679. | Refereed –Journal Articles | 2005 | |||
| 77 | Susie Stephens, Jake Y. Chen, and Shiby Thomas (2004) ODM BLAST: Sequence Homology Search in the RDBMS. IEEE Data Engineering Bulletin, Vol. 27, Issue 3, pp. 20-23. | Refereed –Journal Articles | 2004 | |||
| 78 | Jake Y. Chen* (2004) Book Review: Digital Code of Life—How Bioinformatics is Revolutionizing Science, Medicine, and Business. Briefings in Bioinformatics, Vol. 5, Issue 3, pp. 305-307. | Refereed –Journal Articles | 2004 | |||
| 79 | Jake Y. Chen* and John Carlis (2003) Genomic Data Modeling. Information Systems, Vol. 28, Issue 4: (Special Issue on Data Management in Bioinformatics), pp. 287-310. | Refereed –Journal Articles | 2003 |
| Number | Name | Type | Year | Researchgate | Endnote | |
|---|---|---|---|---|---|---|
| 1 | Jake Chen*, Michael Neylon, Zongliang Yue, Thanh Nguyen, Timothy Ratliff (2016) Towards Constructing “Super Gene Sets” Regulatory Networks, Proceedings of the 2016 International Conference on Bioinformatics & Biomedicine, Shenzhen, China, doi: 10.1109/BIBM.2016.7822534. | Conference or Workshop Proceedings Articles | 2016 | |||
| 2 | Ni Cao, Sisi Zeng, Feixia Shen, Chuandi Pan, Chengshui Chen, Thanh Nguen, and Jake Chen* (2015) Predictive and Preventive Models for Diabetes Prevention using Clinical Information in Electronic Health Record, Proceedings of the 2015 International Conference on Bioinformatics & Biomedicine, Washington, DC, pp. 867-874. | Conference or Workshop Proceedings Articles | 2015 | |||
| 3 | Thanh Nguyen, Junjie Chen, Dongxiang Ji, Xiaoru Sun, Chuandi Pan,* Chengshui Chen*, and Jake Y. Chen* (2015) An Integrated Machine Learning and Network Analysis to Discover Marker Clinical Measurement in Lung Cancer, Proceedings of 2015 International Conference on Genome Medicine, eds. Le L & Pham S, Ho Chi Minh City, Viet Nam. | Conference or Workshop Proceedings Articles | 2015 | |||
| 4 | Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen* (2014) Constructing Regulatory Gene Set Network to Reveal Novel Insights into Biological Systems, Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and medical Sciences, Miami Beach, FL, doi: 10.1109/ICCABS.2014.6863927. | Conference or Workshop Proceedings Articles | 2014 | |||
| 5 | Xiaogang Wu and Jake Chen* (2012) An Evaluation for Merging Signaling Pathways by Using Protein-Protein Interaction Data, Proceedings of IEEE International Workshop on Genomic Signal Processing and Statistics, Washington, DC. | Conference or Workshop Proceedings Articles | 2012 | |||
| 6 | David Johnson, Brandon Shafer, Jaehwan John Lee, and Jake Chen* (2012) Multi-Biomarker Panel Selection on a GPU, Proceedings of IEEE International Conference on Electro/Information Technology, Indianapolis, IN. | Conference or Workshop Proceedings Articles | 2012 | |||
| 7 | Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christopher Reinhard, Shuyu D. Li, Jake Y. Chen* (2012) Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays, Proceedings of the Eighth Annual International Symposium on Integrative Bioinformatics, Hangfzhou, Zhejiang, China. | Conference or Workshop Proceedings Articles | 2012 | |||
| 8 | Liang-Chin Huang and Jake Y. Chen* (2011) A Network Biology Approach to Predicting Drug Cardiotoxicity, Proceedings of the International Conference on Bioinformatics & Biomedicine, Atlanta, GA, pp. 278-281. | Conference or Workshop Proceedings Articles | 2011 | |||
| 9 | Jason McLaughlin, Qian You, Shiaofen Fang, and Jake Y. Chen* (2011) TAO: Terrain Analytic Operators for Expert-Guided Data Mining Applications, Workshop on Visual Analytics in Healthcare, Providence, RI. | Conference or Workshop Proceedings Articles | 2011 | |||
| 10 | Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne Mckenzie, Sunil Badve, and Jake Y. Chen* (2011) Predicting Drug Efficacy Based on the Integrated Breast Cancer Pathway Model, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX. | Conference or Workshop Proceedings Articles | 2011 | |||
| 11 | Xiaogang Wu and Jake Y. Chen* (2011) Network Reordering Based Integrative Expression Profiling for Microarray Classification, 2011 Great Lakes Bioinformatics Conference, Athens, OH. | Conference or Workshop Proceedings Articles | 2011 | |||
| 12 | Xukai Zou*, Peng Liu*, and Jake Y. Chen* (2011) Personal Genome Privacy Protection with Feature-based Hierarchical Dual-stage Encryptions, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX. | Conference or Workshop Proceedings Articles | 2011 | |||
| 13 | Fan Zhang and Jake Y. Chen* (2010) Novel Protein Isoform Biomarker Identifications from Proteomes, 2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong. | Conference or Workshop Proceedings Articles | 2011 | |||
| 14 | Hui Huang, Xiaogang Wu, Shuyu Li, Sara Ibrahim, Taiwo Ajumobi, and Jake Y. Chen* (2010) Evaluate Drug Effects on Gene Expression Profiles with Connectivity Maps, 2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong. | Conference or Workshop Proceedings Articles | 2010 | |||
| 15 | Fan Zhang and Jake Y. Chen* (2010) Proteome-scale Protein Isoform Characterization with High Performance Computing, 2010 Microsoft eScience Workshop Proceedings, Berkeley, CA. | Conference or Workshop Proceedings Articles | 2010 | |||
| 16 | Fengjun Li, Jake Y. Chen, Xukai Zou, and Peng Liu (2010) New Privacy Threats in Healthcare Informatics: When Medical Records Join the Web, Ninth ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2010) at the International Conference on Knowledge Discovery and Data Mining, Washington, DC. (Acceptance rate: 37%) | Conference or Workshop Proceedings Articles | 2010 | |||
| 17 | Fan Zhang, Mu Wang, and Jake Y. Chen* (2010) Breast Cancer Plasma Protein Biomarker Discovery by Coupling LC-MS/MS Proteomics and Systems Biology, Proceedings of the ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY. (poster paper; accepted) | Conference or Workshop Proceedings Articles | 2010 | |||
| 18 | Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen* (2010) Random Walk Ranking Guided by Disease Association Networks for Lung Cancer Biomarker Discovery, Proceedings of the International Symposium on Biocomputing, Vol. 1, No. 33, pp. 1-8. (Acceptance rate: 30%) | Conference or Workshop Proceedings Articles | 2010 | |||
| 19 | Jieun Jeong and Jake Y. Chen* (2009) RIC: Ranking with Interaction Chains and its Applications in Computational Clinical Proteomics Studies, Proceedings of the International Conference on Bioinformatics & Biomedicine, pp. 216-221. (Acceptance rate: 17% out of 256 submissions) | Conference or Workshop Proceedings Articles | 2009 | |||
| 20 | Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen* (2009) SWRWR: Seed-weighted Random Walks Ranking Method and Its Application to Leukemia Cancer Biomarker Prioritizations, IEEE International Conference on Bioinformatics and Biomedicine Workshop 2009, pp. 220-225. (Acceptance rate: <35%) | Conference or Workshop Proceedings Articles | 2009 | |||
| 21 | Fan Zhang and Jake Y. Chen* (2009) A Neural Network Approach to Multi-biomarker Panel Development Based on LC/MS/MS Proteomics Profiles: A Case Study in Breast Cancer, Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems, pp. 1-6, doi: 10.1109/CBMS.2009.5255456. | Conference or Workshop Proceedings Articles | 2009 | |||
| 22 | Hui Huang, Jiao Li, and Jake Y. Chen* (2009) Disease Gene-fishing in Molecular Interaction Networks: a Case Study in Colorectal Cancer, Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419. | Conference or Workshop Proceedings Articles | 2009 | |||
| 23 | Xiaogang Wu, Ragini Pandey, and Jake Y. Chen* (2009) Network Topological Reordering Revealing Systemic Patterns in Yeast Protein Interaction Networks, Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419. | Conference or Workshop Proceedings Articles | 2009 | |||
| 24 | Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Vaka, and Jake Y. Chen* (2009) Visualizing a Correlative Multi-level Graph of Biology Entity Interactions, Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp.304-309. | Conference or Workshop Proceedings Articles | 2009 | |||
| 25 | John Springer and Jake Y. Chen* (2009) Toward Ontology-Driven Omics Data Integration in Current Database Management Systems, Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp. 292-297. | Conference or Workshop Proceedings Articles | 2009 | |||
| 26 | Jiao Li, Pamela Crowell, and Jake Y. Chen* (2009) Construct Anticancer Drug-Drug Correlation Network, Proceedings of the 24th Annual ACM Symposium on Applied Computing, Vol. 2, pp. 771-775. (Acceptance rate: 28%) | Conference or Workshop Proceedings Articles | 2009 | |||
| 27 | Mingyi Wang and Jake Y. Chen* (2008) Gene Selection using the GMM-IG Framework based Integrative Analysis. IEEE Proceedings of the International Conference on Biomedical Engineering and Informatics, Vol.1, pp. 292-296. (Acceptance rate: ~30%, out of >700 submissions) | Conference or Workshop Proceedings Articles | 2008 | |||
| 28 | Harini Kasamsetty, Xiaogang Wu, and Jake Y. Chen* (2008) An Integrative Human Pathway Database for Systems Biology Applications. Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1297-1301. (Acceptance rate: 24%, 9 out of 38 submissions for BIO track) | Conference or Workshop Proceedings Articles | 2008 | |||
| 29 | Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* (2008) Mining Disease-Specific Molecular Association Profiles from Biomedical Literature: A Case Study. Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1287-1291. (Acceptance rate: 24%, 9 out of 38 submissions for BIO track) | Conference or Workshop Proceedings Articles | 2008 | |||
| 30 | Jake Y. Chen*, Changyu Shen, Zhong Yan, Dawn P. G. Brown, and Mu Wang (2006) A Systems Biology Case Study of Ovarian Cancer Drug Resistance. Computational Systems Bioinformatics: CSB2006 Conference Proceedings, edited by Peter Markstein and Ying Xu, Series on Advances in Bioinformatics and Computational Biology, Vol. 4, pp. 389-398. (Acceptance rate: 19%, out of 154 submissions) | Conference or Workshop Proceedings Articles | 2006 | |||
| 31 | Jake Y. Chen*, Sarah L. Pinkerton, Changyu Shen, and Mu Wang (2006) An Integrated Computational Proteomics Method to Extract Protein Targets for Fanconi Anemia Studies. Proceedings of the 21st Annual ACM Symposium on Applied Computing, Dijon, France, Vol. I, pp. 173-179. (Acceptance rate: 32%) | Conference or Workshop Proceedings Articles | 2006 | |||
| 32 | Jake Y. Chen*, Changyu Shen, and Andrey Sivachenko (2006) Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data. Pacific Symposium on Biocomputing, Vol. 11, pp. 367-378. (Acceptance rate: 20%) | Conference or Workshop Proceedings Articles | 2006 | |||
| 33 | Changyu Shen, Lang Li, Jake Y. Chen* (2005) Discover True Association Rates in Multi-protein Complex Proteomics Data Sets. Proceedings of the IEEE Computational Systems Biology Bioinformatics Conference, Stanford University, Stanford, CA, Vol. 1, pp. 167-174. (Acceptance rate: 12%, out of 246 submissions) | Conference or Workshop Proceedings Articles | 2005 | |||
| 34 | Jake Y. Chen*, John Carlis, and Ning Gao (2005) A Method for Conquering Complex Biological Database Queries. Proceedings of the 20th Annual ACM Symposium on Applied Computing, Santa Fe, NM, Vol. I, pp. 110-114. (Acceptance rate: 35%) | Conference or Workshop Proceedings Articles | 2005 | |||
| 35 | Jake Y. Chen* (2004) Experience with Processing and Exploration of High-throughput Protein Interaction Data, Session on Systems Biology and Bioinformatics. Proceedings of the Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, Vol. VII, pp. 41-45. | Conference or Workshop Proceedings Articles | 2004 | |||
| 36 | Jake Y. Chen*, Andrey Y. Sivachenko, and Lang Li (2004) High-throughput Protein Interactome Data: Minable or Not? Fourth ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2004) at the International Conference on Knowledge Discovery and Data Mining, Seattle, WA, pp. 18-23. (Acceptance rate: 38%) | Conference or Workshop Proceedings Articles | 2004 | |||
| 37 | Jake Y. Chen*, Andrey Y. Sivachenko, Russell Bell, Connie Kurschner, Irene Ota, and Sudhir Sahasrabudhe (2003) Initial Large-scale Exploration of Protein-protein Interactions in the Human Brain. Proceedings of the IEEE CSB Bioinformatics Conference, Stanford University, Stanford, CA, published by IEEE Computer Society Press, pp. 229-234. (Acceptance rate: 18%) | Conference or Workshop Proceedings Articles | 2003 | |||
| 38 | Jake Y. Chen* and John Carlis (2003) Similar_Join: Extending DBMS with a Bio-specific Operator. Proceedings of the 18th ACM Symposium on Applied Computing, Melbourne, Florida, pp. 109-114. (Acceptance rate: 33%) | Conference or Workshop Proceedings Articles | 2003 | |||
| 39 | Jake Y. Chen* and John Carlis (2002) Managing Bioinformatics Challenges in Expression Microarray Sequence Selection Projects. Proceedings of the Second Chinese Conference on Bioinformatics, Beijing, China. | Conference or Workshop Proceedings Articles | 2002 | |||
| 40 | Jake Y. Chen* and John Carlis (2002) A High-density Microarray Case Study of Query Modeling In Bioinformatics. Proceedings of the International Conference on Bioinformatics 2002, Bangkok, Thailand. | Conference or Workshop Proceedings Articles | 2002 | |||
| 41 | Yue Chen*, Libby Shoop, John Carlis, and John Riedl (2001) A High-throughput System to Resolve Inconsistent Reading Frame Predictions for Expressed Sequence Tags. Proceedings of Workshop on Inconsistency in Data and Knowledge at the International Joint Conference on Artificial Intelligence (IJCAI), Seattle, WA. | Conference or Workshop Proceedings Articles | 2001 |
| Number | Name | Type | Year | Researchgate | Endnote | |
|---|---|---|---|---|---|---|
| 1 | Xin Gao, Jake Y. Chen, and Mohammed Zaki, ed. (2018) Special Issue on BIOKDD Workshop 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2018 | |||
| 2 | Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki, ed. (2015) IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2015 | |||
| 3 | Jake Y. Chen and Vasant Honavar, ed. (2014) Proceedings of IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences. IEEE. | Edited Conference Proceedings and Journal Special Issues | 2014 | |||
| 4 | Sarath Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed Zaki, ed. (2014) Proceedings of the Thirteenth International Workshop on Data Mining in Bioinformatics. ACM 2014. | Edited Conference Proceedings and Journal Special Issues | 2014 | |||
| 5 | Gaurav Pandey, Huzefa Rangwala, George Karypis, Jake Y. Chen, and Mohammed Zaki, ed. (2013) Proceedings of the Twelfth International Workshop on Data Mining in Bioinformatics. ACM 2013, ISBN 978-1-4503-2327-7. | Edited Conference Proceedings and Journal Special Issues | 2013 | |||
| 6 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2012) Special Issue on Data Mining for Biomarker Discovery, International Journal of Data Mining in Bioinformatics. | Edited Conference Proceedings and Journal Special Issues | 2012 | |||
| 7 | Tamer Kahveci, Saeed Salem, Mehmet Koyuturk, Jake Y. Chen, and Mohammed Zaki, ed. (2012) Proceedings of the Eleventh International Workshop on Data Mining in Bioinformatics. ACM 2012, ISBN 978-1-4503-1552-4. | Edited Conference Proceedings and Journal Special Issues | 2012 | |||
| 8 | Jake Y. Chen, Mohammed Zaki, Mohammad Hasan, and Jun Huan, ed. (2011) Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2011 | |||
| 9 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2010) Proceedings of the Second International Workshop on Data Mining in Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2010 | |||
| 10 | Luke Huan, Jake Y. Chen, and Mohammed Zaki, ed. (2010) Proceedings of the Ninth International Workshop on Data Mining in Bioinformatics. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2010 | |||
| 11 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2009) Proceedings of the International Workshop on Data Mining in Bioinformatics. 34 pages. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2009 | |||
| 12 | Stefano Lonardi and Jake Y. Chen, ed. (2008) Special Issue on Data Mining in Bioinformatics (BIOKDD 2007), Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6. | Edited Conference Proceedings and Journal Special Issues | 2008 | |||
| 13 | Stefano Lonardi, Jake Y. Chen, and Mohammed Zaki, ed. (2008) Proceedings of the Eighth International Workshop on Data Mining in Bioinformatics. 70 pages. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2008 | |||
| 14 | Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang and Jake Y. Chen, ed. (2007) Special Issue on Ontologies for Bioinformatics, International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3. | Edited Conference Proceedings and Journal Special Issues | 2007 | |||
| 15 | Jake Y. Chen, Stefano Lonardi, and Mohammed Zaki, ed. (2007) Proceedings of the Seventh International Workshop on Data Mining in Bioinformatics. 87 pages. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2007 | |||
| 16 | Katsuhisa Horimoto, Jake Chen, and Amy Chan, ed. (2004) Applications of Informatics and Cybernetics in Science and Engineering, Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics (Vol. VII). ISBN: 980-6560-13-2. | Edited Conference Proceedings and Journal Special Issues | 2004 |
| Number | Name | Researchgate | Endnote | Type | Year | |
|---|---|---|---|---|---|---|
| 1 | Jake Y. Chen and Stefano Lonardi, ed. (2009) Biological Data Mining. 656 pages. Published by Chapman & Hall/CRC, USA. ISBN: 978-1420086843. | Book | 2009 | |||
| 2 | Jake Y. Chen and Amandeep Sidhu, ed. (2007) Biological Database Modeling. 224 pages. Published by Artech House, Boston, MA, USA. ISBN: 978-1596932586. | Book | 2007 | |||
| 3 | Fan Zhang, Xiaogang Wu, and Jake Y. Chen* (2013) Computational Biomarker Discovery. Approaches in Integrative Bioinformatics – Towards Virtual Cell, pp. 355-386 | Refereed – Chapters | 2013 | |||
| 4 | Jake Y. Chen*, Heng Xu*, Pan Shi, Adam Culbertson, and Eric Meslin (2011) Ethics and Privacy Issues for Systems Biology Application in Predictive and Personalized Medicine. Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, pp. 1-27. | Refereed – Chapters | 2011 | |||
| 5 | Fan Zhang and Jake Y. Chen* (2011) Data Mining Methods in Omics-based Biomarker Discovery. Bioinformatics for Omics data: Methods and Protocols, pp. 511-526. | Refereed – Chapters | 2011 | |||
| 6 | Jake Y. Chen* and Tianxiao Huan (2010) ProteoLens: A Database-driven Visual Data Mining Tool for Network Biology. Systems Biology for Signaling Networks, pp. 857-876. | Refereed – Chapters | 2010 | |||
| 7 | Jieun Jeong and Jake Y. Chen* (2010) Techniques for Prioritization of Disease Genes. Computational Intelligence and Pattern Analysis in Biological Informatics, pp. 309-324. | Refereed – Chapters | 2010 | |||
| 8 | Jake Y. Chen*, Shailaja Taduri, and Frank Lloyd (2009) Design of an Online Physician-Mediated Personal Health Record System. Biomedical Data and Applications, Studies in Computational Intelligence, Vol. 224, pp. 265-279. | Refereed – Chapters | 2009 | |||
| 9 | Jake Y. Chen, Eunseog Youn, Sean D Mooney* (2009) Connecting Protein Interaction Data, Mutations and Disease using Bioinformatics. Methods in Molecular Biology: Computational Systems Biology, pp. 449-462. | Refereed – Chapters | 2009 | |||
| 10 | Xiaogang Wu and Jake Y. Chen* (2009) Molecular Interaction Networks: Topological and Functional Characterizations. Automation in Genomics and Proteomics: An Engineering Case-Based Approach, pp. 145-175. | Refereed – Chapters | 2009 | |||
| 11 | Amandeep Sidhu and Jake Y. Chen* (2007) Basic Concepts. Biological Database Modeling. Published by Artech House, pp. 1-8. | Refereed – Chapters | 2007 | |||
| 12 | Zhong Yan, Jake Y. Chen*, Josh Heyen, Lee W Ott, Cary Woods, Maureen A Harrington, and Mark G Goebl (2007) Data Management in Expression-based Proteomics. Biological Database Modeling. Published by Artech House, pp. 143-162. | Refereed – Chapters | 2007 | |||
| 13 | SudhaRani Mamidipalli and Jake Y. Chen* (2007) Protein-Protein Interactions: Concepts, Databases, Software Tools, and Biomedical Implications. Current Topics in Human Genetics: Studies of Complex Diseases. Published by World Scientific Publishing Co., pp. 539-562. | Refereed – Chapters | 2007 | |||
| 14 | Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee (2016) DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics. Proceedings of ACM 2016 Conference on Information and Knowledge Management, pp. 2511-2512. | Editorial Articles in Books/Proceedings | 2016 | |||
| 15 | Mohammad Al Hasan, Luke Huan, Jake Y. Chen, and Mohammed Zaki (2011) BIOKDD’11: Workshop on Data Mining in Bioinformatics. Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2011 | |||
| 16 | Luke Huan, Jake Y. Chen, and Mohammed Zaki (2010) BIOKDD’10: Workshop on Data Mining in Bioinformatics. Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2010 | |||
| 17 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen (2009) Data Mining for Biomarker Discovery: The Time is Ripe. IEEE International Conference on Bioinformatics and Biomedicine Workshop 2009, pp. 195-196. | Editorial Articles in Books/Proceedings | 2009 | |||
| 18 | Jake Y. Chen and Stefano Lonardi (2009) Preface. Biological Data Mining, pp. ix-xii. | Editorial Articles in Books/Proceedings | 2009 | |||
| 19 | Stefano Lonardi, Jake Y. Chen, and Mohammed Zaki (2008) Editorial: 2008 International Workshop on Data Mining in Bioinformatics. Proceedings of the Eighth International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2008 | |||
| 20 | Jake Y. Chen and Amandeep Sidhu (2007) Preface. Biological Database Modeling, pp. vii-x. | Editorial Articles in Books/Proceedings | 2007 | |||
| 21 | Jake Y. Chen, Stefano Lonardi, and Mohammed Zaki (2007) Editorial: BIOKDD ‘07: Workshop on Data Mining in Bioinformatics. Proceedings of the Seventh International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2007 | |||
| 22 | Jake Y. Chen and Bradley S. Sherman (2005) Session Editorial: Computer Infrastructure for Systems Biology. Proceedings of the 18th International Conference on Systems Engineering. Published by IEEE Computer Society Press, pp. 283-285. | Editorial Articles in Books/Proceedings | 2005 | |||
| 23 | Warren T. Jones, Mathew J. Palakal, and Jake Y. Chen (2004) Editorial Message: Special Track on Bioinformatics. Proceedings of the 2004 ACM Symposium on Applied Computing, Nicosia, Cyprus, p. 101. | Editorial Articles in Books/Proceedings | 2004 |